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Phylogeography and Resistome Epidemiology of Gram-Negative Bacteria in Africa: A

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Phylogeography and Resistome Epidemiology of Gram-Negative Bacteria in Africa: A medRxiv preprint doi: https://doi.org/10.1101/2020.04.09.20059766; this version posted April 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Phylogeography and Resistome Epidemiology of Gram-Negative Bacteria in Africa: A Systematic Review and Genomic Meta-Analysis from a One-Health Perspective John Osei Sekyere#1 and Melese Abate Reta1 Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa1 #Address correspondence to: Dr. John Osei Sekyere, Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa. Email: [email protected]; [email protected] Tel. +27- (0)12-319-2251 Running head: Epidemiology of Gram-negative bacterial resistance, Africa Highlights/Significance Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Herein, we used different methods to map out the geographical hotspots, sources and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonnorhoeae, Vibrio cholerae, Campylobacter jejuni etc. were common pathogens shuttling AR genes. Transmission of same clones/strains across countries and between animals, humans, plants and the environment were observed. We recommend Enterobacter spp. or K. pneumoniae as better model/index organisms for AR surveillance. NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.04.09.20059766; this version posted April 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Objectives/Backgrounds: Antibiotic resistance (ABR) remains a major threat to public health and infectious disease management globally. However, ABR ramifications in developing countries is worsened by limited molecular diagnostics, expensive therapeutics, inadequate skilled clinicians and scientists, and unsanitary environments. Methods: Data on specimens, species, clones, resistance genes, mobile genetic elements, and diagnostics were extracted and analysed from English articles published between 2015 and December 2019. The genomes and resistomes of the various species, obtained from PATRIC and NCBI, were analysed phylogenetically using RAxML and annotated with Figtree. The phylogeography of resistant clones/clades was mapped manually. Results & conclusion: Thirty species from 31 countries and 24 genera from 41 countries were respectively analysed from 146 articles and 3028 genomes. Genes mediating resistance to β-lactams (including blaTEM-1, blaCTX-M, blaNDM, blaIMP, blaVIM, blaOXA-48/181), fluoroquinolones (oqxAB, qnrA/B/D/S, gyrA/B and parCE mutations etc.), aminoglycosides (including armA, rmtC/F), sulphonamides (sul-1/2/3), trimethoprim (dfrA), tetracycline (tet(A/B/C/D/G/O/M/39)), colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in Enterobacter spp. and K. pneumoniae, and also in Serratia marcescens, Escherichia coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc. on mostly IncF-type, IncX3/4, ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion sequences and transposons. Clonal and multiclonal outbreaks and dissemination of resistance genes across species, countries and between humans, animals, plants and the environment were observed; E. coli ST103, K. pneumoniae ST101, S. enterica ST1/2 and V. cholerae ST69/515 were common strains. Most pathogens were of human origin and zoonotic transmissions were relatively limited. One Health studies in Africa are needed. [2] medRxiv preprint doi: https://doi.org/10.1101/2020.04.09.20059766; this version posted April 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Keywords: One Health; Antibiotic resistance; molecular epidemiology; diagnostics; genomics; resistome; mobilome; Africa Introduction Antibiotic resistance (ABR), particularly in Gram-Negative bacteria (GNB), is complicating infection management in Africa and the rest of the world as it restricts effective therapeutic options available to clinicians in human and veterinary medicine 1–3. Given the unsanitary environments common in developing countries as well as the limited healthcare and laboratory facilities, poor sewage management, high patient-to-physician ratios, little or no regulation on antibiotic usage etc., the escalation of ABR in developing countries (Africa) is precarious 3–5. Coupled with these is the limited funding available for molecular surveillance of ABR to map out the true burden of the problem 2,4. A recent global metagenomic survey, for instance, found that African countries had the highest ABR genes (ARGs) abundance, although in Animals, Asia was found to have more ABR hotspots than Africa 2,5. Together, GNB cause or aggravate some of the most fatal and common infections and diseases known to mankind: sepsis, meningitis/meningococcemia, gonorrhoea, pneumonia, cystic fibrosis, urethritis, pelvic inflammatory disease, cholera, typhoid, whooping cough, diarrhoea etc6–15. It is worth noting that compared to Gram-positive bacteria, GNB has been implicated in the development of more resistance mechanisms, including resistance to last- resort antibiotics such as colistin (mcr), carbapenems (blaNDM, blaVIM, blaKPC, blaIMP, blaGES etc.) and tigecycline (tet(X)) 1,16,17. Moreover, these ARGs are found in more diverse GNB species and genera, with substantial mortalities, morbidities and multi-drug resistance 16–19. Hence, GNB species such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Enterobacteriaceae expressing resistance to carbapenems and extended-spectrum β- lactamases (ESBLs) are respectively classified as critical and high priority pathogens by the WHO 20,21. [3] medRxiv preprint doi: https://doi.org/10.1101/2020.04.09.20059766; this version posted April 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. The presence of these ARGs and species in human, environmental and animal specimens in Africa (and globally) are well documented, strengthening the call for further One Health molecular surveillance 2,3,5,22. Yet, a systematic review on GNB in Africa from a One Health perspective is lacking 22,23. This limits the comprehensive appreciation of the epidemiology of ARGs across the continent. Herein, we further undertake a detailed phylogenomic, phylogeographic and resistome analyses using publicly available genomes to augment the findings in the literature and describe the evolutionary epidemiology of ARGs in Africa. Methods Databases and Search Strategy A comprehensive literature search was carried out on PubMed and/or ResearchGate, ScienceDirect and Web of Science electronic databases. English research articles published between January 2015 and December 2019 were retrieved and screened using the following search terms and/or phrases: "molecular epidemiology", "gram-negative bacteria"; "mechanisms of resistance"; antimicrobial resistance genotypes"; "drug resistance"; "AMR genotypes"; "genetic diversity"; "clones"; "genotyping"; "antibiotic resistance gene"; "plasmid"; "mobile genetic elements"; "resistome"; "gene mutation"; "frequency of resistance gene mutation"; and Africa. The search terms used were further paired with each other or combined with the name of each African country, and searching strings were implemented using "OR" and "AND" Boolean operators. Inclusion and Exclusion Criteria Articles addressing the molecular mechanisms (using PCR, microarray or WGS) of ABR in GNB and undertaking bacterial typing (MLST, PFGE, ERIC-PCR, WGS etc.) were included in this systematic review. Papers which addressed ABR using only disc diffusion, broth microdilution, E-test, Vitek, MicroScan etc. without a molecular (PCR/microarray/WGS) [4] medRxiv preprint doi: https://doi.org/10.1101/2020.04.09.20059766; this version posted April 14, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. analyses of the underlying resistance mechanism and typing (clonality) of the isolates were excluded. Included data This review was carried out using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (Figure 1). The following data were extracted from the included articles: country; study year; specimen type and source/s; sample size; total isolates (isolation rate); total isolates for which antimicrobial sensitivity testing (AST) was determined; bacterial
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